I’m a big fan of Plan-G for flight planning. It can be used with FSX, P3D, X-Plane, etc. One of the nice features it has is that it can connect to your running sim (either locally or remotely), and you can track your movements around the world, and see the AI (and/or MP) planes. It can even connect to VATSIM (although I suspect that requires a running VATSIM client. I’ve never used one so I don’t know).
One of the drawbacks is that Plan-G doesn’t understand real world routing information (such as those provided by FlightAware.
I found a nifty site called SimBrief (Free!) that allows fairly complex flight planning. You can essentially take a real-world route from FlightAware and paste it in to the routing in SimBrief, and then download a sim-compatible flight plan (it supports various sims). You can then open the flight plan in plan-g, fix any problems (sometimes a waypoint will be WAAAAY off), and then export a new FSX flight plan once you’re done fiddling.